Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Xbp1

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
Liver
strain
C57BJ/L6 background
genotype
Xbp1 flx/flx (WT, wild-type)
gender
male
age
12-16 weeks
tissue
Liver
time point
CT04
antibody
anti-XBP1s (Biolegend Poly6195)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The comprehensive CT0 and CT8 DNA libraries were prepared at the MD Anderson Cancer Center, which generated ~40 million 75 bp paired-end reads per samples. The CT0 to CT36 time point DNA libraries were prepared at the University of Houston Sequencing Core and generated ~30 million 75 bp single-end reads per sample. DNA libraries generated from 1ng input DNA were prepared with KAPA Hyper Prep Kit (KAPABIOSYSTEMS) for the comprehensive CT0 and CT8 DNA libraries and with Ovation® Ultralow V2 DNA-Seq library preparation kit (NuGen) for the CT0 to CT36 time point DNA libraries. The size selection was performed using SPRIselect beads (Beckman Coulter), followed by quality control analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent). The DNA libraries were pooled and sequenced using NextSeq 500 (Illumina).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
45459022
Reads aligned (%)
96.5
Duplicates removed (%)
4.0
Number of peaks
242 (qval < 1E-05)

mm9

Number of total reads
45459022
Reads aligned (%)
96.4
Duplicates removed (%)
4.1
Number of peaks
205 (qval < 1E-05)

Base call quality data from DBCLS SRA